The John Day is the longest river entirely in the state of Oregon at 281 miles. The most popular floating section is about 100 miles long, through northern Wheeler County, then again as the river forms the county lines between Wheeler-Wasco and Gilliam-Sherman. It passes through no towns in this section.

Most users are out for fishing, desert scenery and solitude. The river is not known for big whitewater, though it should not be taken lightly. Clarno Rapids is the only Class III rapids in the sections that will have limited use.

The Prineville BLM also manages a boaters pass system on the lower Deschutes River, which is the next river west of the John Day. There may be some similarities in the systems, but the John Day permit system will operate independent of the Deschutes.